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2016-07-28guix package: Suggest prefix search path settings.Ludovic Courtès
* guix/scripts/package.scm (build-and-use-profile): Pass #:kind 'prefix to 'display-search-paths'.
2016-07-28gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207].Mark H Weaver
* gnu/packages/patches/gd-CVE-2016-5766.patch, gnu/packages/patches/gd-CVE-2016-6128.patch, gnu/packages/patches/gd-CVE-2016-6132.patch, gnu/packages/patches/gd-CVE-2016-6214.patch, gnu/packages/patches/gd-fix-test-on-i686.patch: Delete files. * gnu/packages/patches/gd-fix-tests-on-i686.patch: New file. * gnu/local.mk (dist_patch_DATA): Update accordingly. * gnu/packages/gd.scm (gd): Update to 2.2.3. [source]: Update patches field accordingly.
2016-07-28gnu: commencement: 'guile-final' is now "hidden".Ludovic Courtès
This way, we no longer have this annoying warning: $ guix build guile -n guix build: warning: ambiguous package specification `guile' guix build: warning: choosing guile-2.0.11 from gnu/packages/guile.scm:128:2 * gnu/packages/commencement.scm (guile-final): Use 'hidden-package'. * tests/packages.scm ("fold-packages, hidden package"): New test.
2016-07-28packages: Add 'hidden-package'.Ludovic Courtès
* guix/packages.scm (hidden-package, hidden-package?): New procedures. * gnu/packages.scm (fold-packages): Filter out 'hidden-package?'. * tests/packages.scm ("hidden-package"): New test.
2016-07-28gnu: Add asciinema.Alex Griffin
* gnu/packages/terminals.scm (asciinema): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-07-28gnu: gnome: Propagate file-roller.Alex Griffin
* gnu/packages/gnome.scm (gnome)[propagated-inputs]: Add file-roller. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-07-28doc: Discourage software bundling.Ludovic Courtès
Fixes <http://bugs.gnu.org/24008>. Suggested by ng0 <ng0@we.make.ritual.n0.is>. * doc/contributing.texi (Submitting Patches): Add item about bundling.
2016-07-28doc: Send changes in your patch which are related.ng0
* doc/contributing.texi (Submitting Patches): New @item: This gives information about sending related changes and examples on what we view as related changes. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2016-07-28doc: Mention separate branch for packages with many dependents.Ludovic Courtès
Suggested by ng0 <ng0@we.make.ritual.n0.is>. * doc/contributing.texi (Submitting Patches): Add note on packages with more than 100 dependents.
2016-07-28gnu: r-genomicfeatures: Update to 1.24.5.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
2016-07-28gnu: r-bsgenome: Update to 1.40.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
2016-07-28gnu: r-iranges: Update to 2.6.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
2016-07-28gnu: r-limma: Update to 3.28.17.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
2016-07-28gnu: r-xvector: Update to 0.12.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
2016-07-28gnu: r-genomicranges: Update to 1.24.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
2016-07-28gnu: r-annotationdbi: Update to 1.34.4.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
2016-07-28gnu: r-biocparallel: Update to 1.6.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
2016-07-28gnu: r-biostrings: Update to 2.40.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
2016-07-28gnu: r-summarizedexperiment: Update to 1.2.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
2016-07-28gnu: r-genomicalignments: Update to 1.8.4.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
2016-07-28gnu: r-rtracklayer: Update to 1.32.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
2016-07-28gnu: r-genomeinfodb: Update to 1.8.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
2016-07-28gnu: r-s4vectors: Update to 0.10.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
2016-07-28gnu: mysql: Update to 5.7.13 [fixes CVE-2016-{3477,3521,3615,5440}].Leo Famulari
* gnu/packages/patches/mysql-fix-failing-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/databases.scm (mysql): Update to 5.7.13.
2016-07-28gnu: the-silver-searcher: Update to 0.32.0.Tomáš Čech
* gnu/packages/code.scm(the-silver-searcher): Update to 0.32.0.
2016-07-27gnu: imagemagick: Update to 6.9.5-3.Leo Famulari
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.5-3.
2016-07-27gnu: mariadb: Update to 10.1.16.Leo Famulari
* gnu/packages/databases.scm (mariadb): Update to 10.1.16.
2016-07-27gnu: calibre: Update to 2.63.0.Alex Griffin
* gnu/packages/ebook.scm (calibre): Update to 2.63.0. [inputs]: Remove unnecessary imagemagick dependency. [phases]: Use modify-phases. * gnu/packages/patches/calibre-drop-unrar.patch: Update for new version. Signed-off-by: Roel Janssen <roel@gnu.org>
2016-07-27system: Source /etc/environment before $HOME/.guix-profile/etc/profile.Carlos Sánchez de La Lama
* gnu/system.scm (operating-system-etc-service) <profile>: Move sourcing of /etc/environment before that of $HOME/.guix-profile/etc/profile. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-07-27gnu: krona-tools: Update to 2.7.Ben Woodcroft
* gnu/packages/web.scm (krona-tools): Update to 2.7. [arguments]: Delete 'build' phase. Install new scripts.
2016-07-27gnu: diamond: Update to 0.8.16.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16.
2016-07-27gnu: guix: Update revision number in version.Andreas Enge
This is a follow-up to commit 95af24a2f1fb58eb9e6ee902c9330534f0aca9f3. Reported by Alex Kost <alezost@gmail.com>.
2016-07-27tests: Use unbuffered input ports when decompressing from 'guix publish'.Ludovic Courtès
Fixes <http://bugs.gnu.org/24060>. Reported by Chris Marusich <cmmarusich@gmail.com>. * tests/publish.scm (http-get-port): Explicitly call 'open-socket-for-uri' and add calls to 'setvbuf'.
2016-07-27zlib: Protect against non-empty port internal buffers.Ludovic Courtès
* guix/zlib.scm (make-gzip-input-port)[gzfile]: Error out if (drain-input port) returns a non-empty string. * guix/zlib.scm (make-gzip-output-port)[gzfile]: Call 'force-output'.
2016-07-27zlib: Clarify when 'gzread!' can return zero.Ludovic Courtès
* guix/zlib.scm (gzread!): Augment docstring to clarify when zero is returned (based on reading zlib code). (make-gzip-input-port)[read!]: Remove scary comment.
2016-07-27gnu: magit: Fix rebase commands that require perl.Alex Griffin
* gnu/packages/emacs.scm (magit)[inputs]: Add 'perl'. [arguments]: Adjust 'patch-exec-paths' phase to make some rebase commands find 'perl'. Signed-off-by: Alex Kost <alezost@gmail.com>
2016-07-27gnu: Add httping.Tobias Geerinckx-Rice
* gnu/packages/networking.scm (httping): New variable.
2016-07-27gnu: Add missing copyright symbol.Tobias Geerinckx-Rice
* gnu/packages/networking.scm: Add missing "©" to header comments.
2016-07-26gnu: gmime: Remove 'gpg' to 'gpg2' substitution.ng0
* gnu/packages/mail.scm (gmime)[arguments]: Remove the substitution which previously changed 'gpg' to 'gpg2' in 'patch-paths-in-tests' phase. Signed-off-by: Leo Famulari <leo@famulari.name>
2016-07-26gnu: dmd: Remove package, superseded by shepherd.Andreas Enge
* gnu/packages/admin.scm (dmd): Remove variable.
2016-07-26gnu: Add perl-db-file.Danny Milosavljevic
* gnu/packages/databases.scm (perl-db_file): New variable. Signed-off-by: Andreas Enge <andreas@enge.fr>
2016-07-26profiles: Output in 'package->manifest-entry' defaults to "out".Ludovic Courtès
Fixes <http://bugs.gnu.org/24029>. Reported by Dylan Jeffers <sapientech@openmailbox.org>. * guix/profiles.scm (package->manifest-entry): Change #:output to default to "out". (packages->manifest): Add 'package?' in second 'match' clause. * tests/profiles.scm ("package->manifest-entry defaults to \"out\""): New test.
2016-07-26environment: Set 'GUIX_ENVIRONMENT' to the profile.Ludovic Courtès
* guix/scripts/environment.scm (create-environment): Set 'GUIX_ENVIRONMENT' to PROFILE. * tests/guix-environment.sh: Test it. * doc/guix.texi (Invoking guix environment): Document it.
2016-07-26import: pypi: Correctly handle new-style URLs.Ludovic Courtès
Fixes <http://bugs.gnu.org/23997>. * guix/import/pypi.scm (guix-package->pypi-name): Rewrite using 'basename' and 'hyphen-package-name->name+version'. * tests/pypi.scm ("guix-package->pypi-name, old URL style") ("guix-package->pypi-name, new URL style"): New tests.
2016-07-26doc: Explain authentication in "System Installation".Ludovic Courtès
Suggested by Vincent Legoll <vincent.legoll@gmail.com>. * doc/guix.texi (OPENPGP-SIGNING-KEY-ID): New constant. (Binary Installation): Use it. (USB Stick Installation): Copy and adjust the authentication bit from "Binary Installation".
2016-07-26doc: Better illustration use of package revision numbers.ng0
* doc/guix.texi (Version Numbers): Add the revision to the example of the git package used in 7.6.3. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-07-26gnu: icecat: Install icons.Alex Griffin
* gnu/packages/gnuzilla.scm (icecat)[arguments]: Add 'install-icons' phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-07-26gnu: Add haveged.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (haveged): New variable.
2016-07-26gnu: Add perceptualdiff.Tobias Geerinckx-Rice
* gnu/packages/image.scm (perceptualdiff): New variable.
2016-07-26gnu: linux-libre@4.1: Update to 4.1.28.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.28.
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